Jing Sun

A plausible scenario for the prebiotic generation of activated RNA substrates under mild aqueous conditions is presented. Using water‐soluble diamidophosphate, in situ production of 2′,3′‐cyclic phosphate‐activated oligoribonucleotides and their subsequent ligation by a ribozyme can be achieved.

Abstract

RNA‐catalyzed RNA ligation is widely believed to be a key reaction for primordial biology. However, since typical chemical routes towards activating RNA substrates are incompatible with ribozyme catalysis, it remains unclear how prebiotic systems generated and sustained pools of activated building blocks needed to form increasingly larger and complex RNA. Herein, we demonstrate in situ activation of RNA substrates under reaction conditions amenable to catalysis by the hairpin ribozyme. We found that diamidophosphate (DAP) and imidazole drive the formation of 2′,3′‐cyclic phosphate RNA mono‐ and oligonucleotides from monophosphorylated precursors in frozen water‐ice. This long‐lived activation enables iterative enzymatic assembly of long RNAs. Our results provide a plausible scenario for the generation of higher‐energy substrates required to fuel ribozyme‐catalyzed RNA synthesis in the absence of a highly evolved metabolism.

Nature Chemistry, Published online: 29 January 2021; doi:10.1038/s41557-020-00624-8

Stimuli-responsive control of drug activation can mitigate issues caused by poor drug selectivity. Now, it has been shown that mechanical force—induced by ultrasound—can be used to activate drugs in three different systems. This approach has enabled the activation of antibiotics or a cytotoxic anticancer agent from synthetic polymers, polyaptamers and nanoparticle assemblies.

Let's work together: A multicomponent environmental system consisting of amino acids, RNA mononucleotides and montmorillonite at various Mg²⁺ concentrations is reported. We show that specific alpha amino acids, especially those that were prebiotically most relevant, act as prebiotic coenzymes and further enhance montmorillonite-catalyzed polymerization in a cooperative mechanism to produce even longer RNA oligomers than the clay alone.

Abstract

Understanding prebiotic RNA synthesis is essential to both the RNA world and RNA-protein co-evolution theories of the origin of life. Nonenzymatic templated RNA synthesis occurs in solution or by montmorillonite clay heterogenous catalysis but the high magnesium concentrations required are deleterious to protocell membranes. Here, we explore a multicomponent environmental system consisting of amino acids, RNA mononucleotides and montmorillonite at various Mg²⁺ concentrations. We show that specific alpha amino acids, especially those that were prebiotically most relevant, act as prebiotic coenzymes and further enhance montmorillonite-catalyzed polymerization in a cooperative mechanism to produce even longer RNA oligomers. Significantly, and different from template-directed nonenzymatic RNA polymerization by primer extension, added Mg²⁺ is not required for montmorillonite-catalyzed polymerization, especially as enhanced by specific amino acids. Thus amino acid specific montmorillonite-catalyzed RNA polymerization is compatible with protocell membranes and could occur in a wider variety of geochemical environments of various Mg²⁺ concentrations.

Nature Nanotechnology, Published online: 18 January 2021; doi:10.1038/s41565-020-00840-w

Self-assembled nanoribbons with extensive and collective intermolecular interactions exhibit robust mechanical properties, enabling their translation to macroscopic solid-state threads.

Dissipative self-assembly driven by chemical fuels is ubiquitous in nature, where it gives rise to a variety of complex structures and functions. A number of synthetic mimics of these natural chemically fueled systems have recently been reported; in parallel, dissipative self-assembly systems fueled by light are being developed. In this perspective, we critically compare chemically and optically driven dissipative self-assembly. Despite the fundamental differences between these two modes of dissipative self-assembly, our analysis reveals that multiple analogies exist between light- and chemically fueled systems.

Reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub‐segments. Now, the structure of this spacer is designed in a rational manner to prevent side‐reactions during MS/MS sequencing and hence enable automated reading of each byte of information in about 100 ms.

Abstract

A major step towards reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub‐segments. However, MS/MS decoding had to be performed manually to safely identify useful fragments of low abundance compared to side‐products from the amide‐based alkoxyamine used. Here, alternative alkoxyamines were designed to prevent side‐reactions and enable automated MS/MS sequencing. Different styryl‐TEMPO spacers were prepared to increase radical delocalization and stiffness of the structure. Their dissociation behavior was investigated by EPR and best results were obtained with spacers containing in‐chain benzyl ring, with no side‐reaction during synthesis or sequencing. Automated decoding of these polymers was performed using the MS‐DECODER software, which interprets fragmentation data recorded for each sub‐segment and re‐align them in their original order based on location tags.

Nature Communications, Published online: 05 January 2021; doi:10.1038/s41467-020-20366-y

Residual stress in crystalline polymers can lead to material failure, but currently methods which can quantify residual stress in such materials are lacking. Here, by using fluorescent-type mechanochromophores, the authors develop a method to visualize and quantify low degrees of stress that arises from micro-mechanical forces during polymer crystallization.

Understanding prebiotic RNA synthesis is essential to both RNA World and RNA‐protein coevolution theories of the Origin of Life. Nonenzymatic templated RNA synthesis occurs in solution or by montmorillonite clay heterogenous catalysis but the high magnesium concentrations required are deleterious to protocell membranes. Here, we explore multicomponent environmental system consisting of amino acids, RNA mononucleotides and montmorillonite at various Mg 2+ concentrations. We show that specific alpha amino acids, especially those that were prebiotically most relevant, act as prebiotic coenzymes and further enhance montmorillonite‐catalyzed polymerization in a cooperative mechanism to produce even longer RNA oligomers. Significantly, and different from template‐directed nonenzymatic RNA polymerization by primer extension, added Mg 2+ is not required for montmorillonite‐catalyzed polymerization, especially as enhanced by specific amino acids. Thus amino acid specific montmorillonite‐catalyzed RNA polymerization is compatible with protocell membranes and could occur in a wider variety of geochemical environments of various Mg 2+ concentrations.

Nature Chemistry, Published online: 22 December 2020; doi:10.1038/s41557-020-00608-8

Fluorinated polyacetylene has typically proven to be inaccessible using traditional polymer synthesis, but there is much interest in its predicted properties. Now, a mechanochemical unzipping strategy has succeeded in the synthesis of a gold-coloured, semiconducting fluorinated polyacetylene with improved stability in air compared to polyacetylene.

Microgels are soft colloids that show responsive behavior and are easy to functionalize for applications. They are considered key components for future smart colloidal material systems. However, so far microgel systems have almost exclusively been studied in classical responsive switching settings using external triggers, while internally organized, autonomous control mechanisms as found in supramolecular chemistry and DNA nanotechnology relying on fuel‐driven out‐of‐equilibrium concepts have not been implemented into microgel systems. Here, we introduce chemically fueled transient volume phase transitions (VPTs) for poly(methacrylic acid) (PMAA) microgels, where the collapsed hydrophobic state can be programmed using the fuel concentration in a cyclic reaction network. We discuss details of the system behavior as a function of pH and fuel amount, unravel kinetically trapped regions and showcase transient encapsulation and time‐programmed release as a first application.

Pumping iron: Mimicking biological out‐of‐equilibrium systems, here a chemically fueled out‐of‐equilibrium material system was demonstrated to generate macroscopic motion such as actuation and lifting objects. This was achieved by driving a lower critical solution temperature (LCST) transition of poly(N‐isopropylacrylamide) (pNIPAAm) hydrogels with heat generated by a copper‐catalyzed azide‐alkyne cycloaddition (CuAAc) reaction.

Abstract

In nature, living systems operate far from equilibrium by consuming and dissipating energy to perform vital processes. Biological systems use chemically derived energy to power out‐of‐equilibrium processes to generate complex macroscopic motion by dissipating energy at the molecular scale. In contrast, it remains a major challenge to create synthetic out‐of‐equilibrium systems that operate on the macroscopic scale. Herein we report a chemically fueled out‐of‐equilibrium system that can perform macroscopic actuation and do work by lifting objects. We achieve this by driving a lower critical solution temperature (LCST) transition of poly(N‐isopropylacrylamide) (pNIPAAm) hydrogels with heat generated by a copper‐catalyzed azide‐alkyne cycloaddition (CuAAc) reaction. Upon completion of the reaction, heat dissipates to the environment, and the system returns to equilibrium, completing one cycle of out‐of‐equilibrium behavior, which can be repeated for multiple cycles by adding new chemical fuels.

Inspired by natural rhodopsin, a natural chromophore retinal guest with visible‐light isomerization was introduced into a solid‐state membrane channel. A novel ethyl‐urea‐derived pillar[6]arene (Urea‐P6) host, capable of selectively binding Cl⁻, was self‐assembled with the retinal guest. Based on the visible‐light‐responsiveness of the host–guest system, Cl⁻ transport can be regulated by visible light between ON and OFF states.

Abstract

Inspired by the light‐regulating capabilities of naturally occurring rhodopsin, we have constructed a visible‐light‐regulated Cl⁻‐transport membrane channel based on a supramolecular host–guest interaction. A natural retinal chromophore, capable of a visible‐light response, is used as the guest and grafted into the artificial channel. Upon introduction of an ethyl‐urea‐derived pillar[6]arene (Urea‐P6) host, threading or de‐threading of the retinal and selective bonding of Cl⁻ can be utilized to regulate ion transport. Based on the visible‐light responsiveness of the host–guest interaction, Cl⁻ transport can be regulated by visible light between ON and OFF states. Visible‐light‐regulated Cl⁻ transport as a chemical model permits to understand comparable biological ion‐selective transport behaviors. Furthermore, this result also supplies a smart visible‐light‐responsive Cl⁻ transporter, which may have applications in natural photoelectric conversion and photo‐controlled delivery systems.

The spatial configuration and optical properties of non‐photoresponsive DNA‐origami‐based plasmonic assemblies can be controlled with light using a photoresponsive medium. Upon exposure to visible light, the medium's pH decreases, inducing the formation of DNA triplex links in the plasmonic assemblies, leading to their spatial reconfiguration, which can be reversed by turning the light off.

Abstract

DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA‐based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non‐photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine‐based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA‐based devices and nanomaterials.

Bioengineered protein fibers were prepared through electrostatic complexation of a positively charged polypeptide and a negatively charged azobenzene‐based surfactant. The photo‐isomerization of the azobenzene moiety from E‐ to Z‐isomer reversibly triggered a modulation of the bulk protein fiber's mechanical performance.

Abstract

Light‐responsive materials have been extensively studied due to the attractive possibility of manipulating their properties with high spatiotemporal control in a non‐invasive fashion. This stimulated the development of a series of photo‐deformable smart devices. However, it remained a challenge to reversibly modulate the stiffness and toughness of bulk materials. Here, we present bioengineered protein fibers and their optomechanical manipulation by employing electrostatic interactions between supercharged polypeptides (SUPs) and an azobenzene (Azo)‐based surfactant. Photo‐isomerization of the Azo moiety from the E‐ to Z‐form reversibly triggered the modulation of tensile strength, stiffness, and toughness of the bulk protein fiber. Specifically, the photo‐induced rearrangement into the Z‐form of Azo possibly strengthened cation–π interactions within the fiber material, resulting in an around twofold increase in the fiber's mechanical performance. The outstanding mechanical and responsive properties open a path towards the development of SUP‐Azo fibers as smart stimuli‐responsive mechano‐biomaterials.

Nature Chemistry, Published online: 30 November 2020; doi:10.1038/s41557-020-00583-0

Mirror-symmetry breaking in chiral systems by a chiral solvent has remained poorly understood for decades. Now, the supramolecular polymerization of triphenylene derivatives has shown that—through the additive effects of polymerization—the cumulative entropic effects of the interactions between chiral solvents and solutes create measurable differences in free enthalpy.

Nature Communications, Published online: 20 November 2020; doi:10.1038/s41467-020-19683-z

Different to exploring molecular topology, the development of supramolecular topology has been limited due to a lack of reliable synthetic methods. Here, the authors describe a supramolecular strategy to access Möbius strips through bending and cyclization of twisted nanofibers self-assembled from chiral glutamate amphiphiles.

Nature Chemistry, Published online: 20 November 2020; doi:10.1038/s41557-020-00580-3

Artificial systems capable of photocatalytic hydrogen production are not typically based on precisely controlled scaffolds. Now, statistical seeded crystallization of block copolymers—bearing either a pendant cobalt catalyst or a photosensitizer—from solution has been shown to yield recyclable, colloidally stable nanofibres that can be tailored to promote photocatalytic hydrogen production from water.

Peptide biosynthesis is performed by ribosomes and several other classes of enzymes, but a simple chemical synthesis may have created the first peptides at the origins of life. α-Aminonitriles—prebiotic α–amino acid precursors—are generally produced by Strecker reactions. However, cysteine’s aminothiol is incompatible with nitriles. Consequently, cysteine nitrile is not stable, and cysteine has been proposed to be a product of evolution, not prebiotic chemistry. We now report a high-yielding, prebiotic synthesis of cysteine peptides. Our biomimetic pathway converts serine to cysteine by nitrile-activated dehydroalanine synthesis. We also demonstrate that N-acylcysteines catalyze peptide ligation, directly coupling kinetically stable—but energy-rich—α-amidonitriles to proteinogenic amines. This rare example of selective and efficient organocatalysis in water implicates cysteine as both catalyst and precursor in prebiotic peptide synthesis.

A series of π‐liquids naphthalene derivatives substituted with chiral branched alkyl chains were designed. Among them, 2,3‐substituted π‐liquid showed both CD and circularly polarized luminescence owing to the formation of chiral aggregates. When achiral anthracene was dissolved in Nap2, the π‐liquid served as chirality and energy transfer media to promote the chiroptical activities in D‐A liquid system. The work unveiled the chiroptical feature of the π‐liquid as a new kind of soft functional materials.

Abstract

The solvent‐free organic π‐liquids have been attracting increasing attentions owing to the inherent optoelectronic properties accompanied by the advantages of non‐volatility and high processability. Herein, we reported a series of naphthalene derivatives substituted with chiral branched alkyl chains, which are present as liquids (Nap1–3) or solid (Nap4) at room temperature, depending on the substitution positions. Circular dichroism (CD) and circularly polarized luminescence (CPL) were only observed for enantiomeric Nap2 (2,3‐substituted) liquid. It is suggested that the chiral aggregation in the π‐liquid leads to the CD signal and the chiral excimer resulting in the CPL performance. When achiral anthracene or pyrene was dissolved in Nap2, the π‐liquid could serve as chirality and energy transfer media in which both CD and CPL emerged from the achiral anthracene. A CPL dissymmetry factor (|g_lum|) of anthracene reached to 5.2×10⁻² when dissolved in chiral Nap2 liquid, which is nearly two orders of magnitude higher than that of the pure Nap2 π‐liquid.